Unlike forests or prairies, which may be destroyed to make way for human development and agriculture, river and stream habitats aren't generally subject to great changes in size. Water quality, not quantity, is the most significant variable in these habitats, and fortunately it has improved over the last twenty years. The content of trace metals in our rivers and streams has plummeted as has the discharge of sewage and factory waste. Some toxins continue to accumulate, however, most notably pesticides, phosphorous, and nitrate nitrogen.
Despite the importance of water quality issues, physical changes do occur in rivers and streams, sometimes to the great detriment of the ecosystem around. Human damming of rivers is the most obvious example, but rechanelling and dredging can also wreak havoc on a river's natural inhabitants.
Perhaps as much as pollution or physical changes, though, the introduction of non-native species, such as the zebra mussel, into Illinois's waterways, has upset the natural balance of the ecosystem. It is estimated that one-fifth of all fish, one-third of all amphibians and reptiles, over half of freshwater mussels, and one-fifth of crayfish have been extirpated or driven into threatened or endangered status in Illinois rivers and streams.